When aides to Mayor Michael R. Bloomberg recently sought backing from City Council members for a key development project, they heard something they were not accustomed to: No.

Normally, Mr. Bloomberg would quickly bring them into line. But on Monday, council members fought him all the way to a humiliating 45-to-1 defeat for one of the mayor’s signature proposals, a $310 million shopping center in the Bronx.

It was the largest project turned down by the Council since Mr. Bloomberg came to office eight years ago, and perhaps the strongest indication yet of the changed landscape the mayor faces a month after his unexpectedly close re-election.

In the past few weeks, Mr. Bloomberg has suffered several setbacks, been forced to modify signature demands and backed down from high-profile fights.

Bowing to neighborhood activists and a languid economy, the mayor retreated from a proposal last week to immediately build housing in a park planned for the Brooklyn waterfront, a feature that aides described as crucial to the project’s future.

To pass a package of environmental rules, the administration dropped an ambitious initiative opposed by real estate interests that would have required landlords to pay to make their buildings more energy efficient.

Over Mr. Bloomberg’s objections, and despite the threat of a veto, the Council overwhelmingly approved laws that would ease parking restrictions.

“If anyone thought there was going to be a third-term honeymoon, the honeymoon has ended before the third term even began,” said Stuart Appelbaum, president of the retail workers’ union, which fought the Bronx retail project.

So after years of largely unchallenged authority, Bloomberg 3.0 is beginning to look like this: a mayor suddenly grappling with emboldened opposition, limits to his influence, a city teeming with economic frustration and residents who are distrustful, in some ways, of a Manhattan billionaire.

“This is a new world now,” said Councilman Bill de Blasio, the city’s public advocate-elect, who built his campaign around the need for a check on Mr. Bloomberg’s power. “He now has to work, as most mayors do, to strike more of a balance and reach a consensus.”

Aides to the mayor dismissed the idea that Mr. Bloomberg had been chastened, pointing to a series of major policy proposals that he has outlined, and battle lines he has drawn, since winning a third term.

He scored a rare victory in Albany with the passage of legislation that would require a new, less expensive pension plan for new city workers. He has vowed to take on the teachers’ union by using student test scores in tenure decisions. And he picked a fight with the Manhattan district attorney, Robert M. Morgenthau, by accusing him of hiding taxpayer dollars in secret bank accounts. But even there, he quickly withdrew from the battle after public criticism.

The aides said the mayor was no less ambitious, nor less firmly wedded to his beliefs today than he was before the election, no matter the size of his victory margin at the polls (for the record, it was 4.6 percent, down from 20 percent in 2005). In several cases, they said, the mayor was yielding to economic realities, not political pressure.

The mayor, said Jason Post, a spokesman, “will continue to make the tough decisions and stand behind key principles, but he has never had a problem with being flexible to help build a better city.”

But aides privately conceded that the city’s political atmosphere has changed.

Two citywide elected offices, the comptroller’s and the public advocate’s, will soon be occupied by Bloomberg skeptics. And a union-backed party that angrily opposed the mayor’s undoing of term limits won a large number of seats on the Council and is eager to flex its muscle on issues of economic populism and projects like the Bronx shopping center.

It is no coincidence that lawmakers from the Bronx led the revolt against the retail project: The borough has the city’s highest unemployment rate, and voters there rejected Mr. Bloomberg in large numbers in November, favoring his Democratic rival, William C. Thompson Jr.

The council members argued that the shopping center, to be built in an abandoned armory, would create low-paying retail jobs that would perpetuate poverty. Since the project was to receive government subsidies, they argued that the city should require retailers to pay a “living wage,” which is nearly three dollars more than the minimum wage.

The mayor’s office rejected imposing a wage requirement on stores, but in negotiations with lawmakers, aides signaled a readiness to use city money to directly or indirectly increase the workers’ pay, according to those involved in the discussions. But the mayor ultimately rejected the plan, wagering that the council members would relent. They did not, and the talks collapsed over the weekend.

The administration said it was standing up for basic business principle: private industry should not be handcuffed by ad hoc government mandates.

“It’s just very disappointing,” the mayor said, “and very bad for the Bronx, a borough that really needs the help.”

The battle was, in many ways, a replay of the mayor’s race, with the union-backed Working Families Party, the retail workers’ union, and the Bronx borough president, Rubén Díaz Jr., fighting the mayor, and the business community and construction workers’ union standing behind Mr. Bloomberg. Even the rhetoric seemed borrowed from the election. Mr. Díaz spoke of “the people prevailing over corporate America.”

The message seemed to resonate with lawmakers outside of the Bronx, who said their constituents had tired of watching the city’s rich get richer while they struggled to cope with higher taxes and fees.

“The fight over the armory is about people who are hurting, saying the developers are going to make money, the city will make money, why not us?” said Councilman James S. Oddo, a Republican from Staten Island.

“Is there any personal pique involved, where people want to score a win against the mayor? Sure, you can’t discount that,” he said. “But for most of us, we just hear every day how much pain people are in.”

Senior aides to Mr. Bloomberg seemed stunned by the defeat. They privately bemoaned the loss of thousands of new jobs in the middle of a deep recession, over what they viewed as a misguided policy debate.

And they fretted over its political meaning. Even the mayor’s close allies in the Council, including the speaker, Christine C. Quinn, voted to kill the project.

Councilman Peter F. Vallone Jr., who endorsed Mr. Bloomberg for re-election, voted against the shopping center on Monday, saying he felt compelled to support his colleagues from the Bronx. With a hint of regret, he called the fight “a harbinger of things to come.”